AdrianCurtin
diff --git a/‎+exploreFNIRS/+connectivity/alignMatrices.m‎
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+function [aligned, masterChannels, masterLabels, nValid] = alignMatrices(results, mode)
+% ALIGNMATRICES Align connectivity results from subjects with different channels
+%
+% Maps each subject's/dyad's connectivity result into a common channel-
+% indexed grid so that matrix entry (i,j) always represents the same
+% channel pair across subjects, regardless of per-subject channel rejection.
+%
+% Syntax:
+%   [aligned, masterCh, masterLabels, nValid] = ...
+%       exploreFNIRS.connectivity.alignMatrices(results, 'union')
+%   [aligned, masterCh, masterLabels, nValid] = ...
+%       exploreFNIRS.connectivity.alignMatrices(results, 'intersection')
+%   [aligned, masterCh, masterLabels, nValid] = ...
+%       exploreFNIRS.connectivity.alignMatrices(results, 0.75)
+%
+% Inputs:
+%   results - Cell array of result structs. Each must have one of:
+%               Connectivity: .matrix [N x N] and .channels [1 x N]
+%               Hyperscanning 'same': .values [N x 1] and .channelsA [1 x N]
+%               Hyperscanning 'all':  .values [Na x Nb] and .channelsA, .channelsB
+%   mode    - Alignment mode:
+%               'union'        - All channels present in any subject (default)
+%               'intersection' - Only channels present in every subject
+%               numeric 0-1    - Channels present in >= mode fraction of subjects
+%
+% Outputs:
+%   aligned       - 3D array with aligned values. NaN where a subject lacks
+%                   data for a channel. Shape: [M x M x K] for connectivity,
+%                   [M x 1 x K] for hyperscanning 'same', [Ma x Mb x K] for 'all'.
+%   masterChannels - Master channel vector (or {masterA, masterB} for 'all' pairing)
+%   masterLabels   - Cell array of labels (or {labelsA, labelsB} for 'all' pairing)
+%   nValid         - Per-cell count of subjects contributing a non-NaN value
+%
+% See also: exploreFNIRS.connectivity.computeMatrix,
+%   exploreFNIRS.hyperscanning.computeGroup
+
+    if nargin < 2
+        mode = 'union';
+    end
+
+    K = length(results);
+    if K == 0
+        error('exploreFNIRS:connectivity:alignMatrices', 'Empty results cell array');
+    end
+
+    % Detect result shape
+    isConnectivity = isfield(results{1}, 'matrix');
+    isHyperAll = ~isConnectivity && isfield(results{1}, 'channelsB') && ...
+        isfield(results{1}, 'values') && ~isvector(results{1}.values);
+
+    if isHyperAll
+        [aligned, masterChannels, masterLabels, nValid] = ...
+            alignHyperscanningAll(results, K, mode);
+    elseif isConnectivity
+        [aligned, masterChannels, masterLabels, nValid] = ...
+            alignConnectivity(results, K, mode);
+    else
+        % Hyperscanning 'same' pairing (vector values)
+        [aligned, masterChannels, masterLabels, nValid] = ...
+            alignHyperscanningSame(results, K, mode);
+    end
+end
+
+
+function [aligned, masterCh, masterLabels, nValid] = alignConnectivity(results, K, mode)
+% Align NxN connectivity matrices
+
+    % Collect all channel vectors
+    allChannels = cell(K, 1);
+    for k = 1:K
+        allChannels{k} = results{k}.channels(:)';
+    end
+
+    masterCh = computeMasterChannels(allChannels, K, mode);
+    M = length(masterCh);
+
+    % Build aligned 3D array
+    aligned = nan(M, M, K);
+    for k = 1:K
+        [~, masterIdx, subIdx] = intersect(masterCh, allChannels{k});
+        aligned(masterIdx, masterIdx, k) = results{k}.matrix(subIdx, subIdx);
+    end
+
+    nValid = sum(~isnan(aligned), 3);
+
+    % Build labels
+    masterLabels = buildLabels(results, masterCh, 'labels', 'channels');
+end
+
+
+function [aligned, masterCh, masterLabels, nValid] = alignHyperscanningSame(results, K, mode)
+% Align Nx1 hyperscanning 'same' pairing vectors
+
+    allChannels = cell(K, 1);
+    for k = 1:K
+        allChannels{k} = results{k}.channelsA(:)';
+    end
+
+    masterCh = computeMasterChannels(allChannels, K, mode);
+    M = length(masterCh);
+
+    aligned = nan(M, 1, K);
+    for k = 1:K
+        [~, masterIdx, subIdx] = intersect(masterCh, allChannels{k});
+        aligned(masterIdx, 1, k) = results{k}.values(subIdx);
+    end
+
+    nValid = sum(~isnan(aligned), 3);
+
+    masterLabels = buildLabels(results, masterCh, 'labelsA', 'channelsA');
+end
+
+
+function [aligned, masterChannels, masterLabels, nValid] = alignHyperscanningAll(results, K, mode)
+% Align Na x Nb hyperscanning 'all' pairing matrices
+
+    allChA = cell(K, 1);
+    allChB = cell(K, 1);
+    for k = 1:K
+        allChA{k} = results{k}.channelsA(:)';
+        allChB{k} = results{k}.channelsB(:)';
+    end
+
+    masterA = computeMasterChannels(allChA, K, mode);
+    masterB = computeMasterChannels(allChB, K, mode);
+    Ma = length(masterA);
+    Mb = length(masterB);
+
+    aligned = nan(Ma, Mb, K);
+    for k = 1:K
+        [~, mIdxA, sIdxA] = intersect(masterA, allChA{k});
+        [~, mIdxB, sIdxB] = intersect(masterB, allChB{k});
+        aligned(mIdxA, mIdxB, k) = results{k}.values(sIdxA, sIdxB);
+    end
+
+    nValid = sum(~isnan(aligned), 3);
+
+    labelsA = buildLabels(results, masterA, 'labelsA', 'channelsA');
+    labelsB = buildLabels(results, masterB, 'labelsB', 'channelsB');
+
+    masterChannels = {masterA, masterB};
+    masterLabels = {labelsA, labelsB};
+end
+
+
+function master = computeMasterChannels(allChannels, K, mode)
+% Compute the master channel set based on alignment mode
+
+    if ischar(mode) || isstring(mode)
+        switch lower(char(mode))
+            case 'union'
+                master = allChannels{1};
+                for k = 2:K
+                    master = union(master, allChannels{k});
+                end
+            case 'intersection'
+                master = allChannels{1};
+                for k = 2:K
+                    master = intersect(master, allChannels{k});
+                end
+            otherwise
+                error('exploreFNIRS:connectivity:alignMatrices', ...
+                    'Unknown alignment mode "%s". Use ''union'', ''intersection'', or a numeric threshold.', char(mode));
+        end
+    elseif isnumeric(mode) && isscalar(mode) && mode > 0 && mode <= 1
+        % Threshold mode: channels in >= mode fraction of subjects
+        all = [];
+        for k = 1:K
+            all = union(all, allChannels{k});
+        end
+        counts = zeros(size(all));
+        for k = 1:K
+            counts = counts + ismember(all, allChannels{k});
+        end
+        master = all(counts >= mode * K);
+    else
+        error('exploreFNIRS:connectivity:alignMatrices', ...
+            'mode must be ''union'', ''intersection'', or a numeric threshold in (0, 1].');
+    end
+
+    master = sort(master(:)');
+end
+
+
+function labels = buildLabels(results, masterCh, labelField, chField)
+% Build labels for master channel set from the first result that has them
+
+    labels = arrayfun(@(c) sprintf('Ch%d', c), masterCh, 'UniformOutput', false);
+
+    for k = 1:length(results)
+        if isfield(results{k}, labelField) && ~isempty(results{k}.(labelField))
+            subCh = results{k}.(chField)(:)';
+            subLabels = results{k}.(labelField);
+            if iscell(subLabels)
+                [~, mIdx, sIdx] = intersect(masterCh, subCh);
+                labels(mIdx) = subLabels(sIdx);
+            end
+            break;
+        end
+    end
+end